BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 038490
         (344 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 35.8 bits (81), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 31/122 (25%), Positives = 57/122 (46%), Gaps = 18/122 (14%)

Query: 102 ALQMFDEMSSFNVQMTVKFFNTLL--------------NPKLTCGKLDRMKELFQIMEKY 147
           AL+++DE     VQ++   +N LL              NP L+ G  D  K++  I++K 
Sbjct: 45  ALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRG-FDIFKQM--IVDKV 101

Query: 148 VSPDACSYNILIHGCVVSRRLEDAWKVFDEMVKRRLQPTLVTFGTLIYGLCLELRVDEAL 207
           V P+  ++       V     E A+ +  +M    +QP L ++G  ++G C +   D+A 
Sbjct: 102 V-PNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAY 160

Query: 208 KL 209
           ++
Sbjct: 161 EV 162



 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/126 (23%), Positives = 60/126 (47%), Gaps = 14/126 (11%)

Query: 205 EALKLKEDIMRVYNVKPDGQVFASLIKGLCAVGE----------LSLALGVKEEMVRDKI 254
           EAL+L ++  R  N     Q   +++  +C++ E          LS    + ++M+ DK+
Sbjct: 44  EALRLYDEARR--NGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKV 101

Query: 255 EMDAGIYSSLIS-ALFKAGRKNEFPAILKEMKERGCKPNSVTYNALISGFCKEEDFEAAF 313
             +   +++    A+ K   +  F  ++K+MK  G +P   +Y   + GFC++ D + A+
Sbjct: 102 VPNEATFTNGARLAVAKDDPEMAFD-MVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAY 160

Query: 314 TILDEM 319
            +   M
Sbjct: 161 EVDAHM 166



 Score = 28.5 bits (62), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 9/115 (7%)

Query: 237 GELSLALGVKEEMVRDKIEMDAGIYSSLI---SALFKAGRKNEFPA------ILKEMKER 287
           G++  AL + +E  R+ +++    Y+ L+   S    A   +  P       I K+M   
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVD 99

Query: 288 GCKPNSVTYNALISGFCKEEDFEAAFTILDEMGDKGCKANPISYNVILGGLCKDG 342
              PN  T+         ++D E AF ++ +M   G +    SY   L G C+ G
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154


>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana, Semet Substituted Form With Sr
          Length = 501

 Score = 35.4 bits (80), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 58/125 (46%), Gaps = 24/125 (19%)

Query: 102 ALQMFDEMSSFNVQMTVKFFNTLL--------------NPKLTCGKLDRMKELFQIMEKY 147
           AL+++DE     VQ++   +N LL              NP L+ G  D  K+   I++K 
Sbjct: 45  ALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRG-FDIFKQX--IVDKV 101

Query: 148 VSPDACSYNILIHGCVVSRRLEDAWKVFDEMVKRR---LQPTLVTFGTLIYGLCLELRVD 204
           V  +A       +G  ++   +D    FD + + +   +QP L ++G  ++G C +   D
Sbjct: 102 VPNEA----TFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157

Query: 205 EALKL 209
           +A ++
Sbjct: 158 KAYEV 162


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.324    0.140    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,162,814
Number of Sequences: 62578
Number of extensions: 408397
Number of successful extensions: 852
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 845
Number of HSP's gapped (non-prelim): 7
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)